Popups are windows, they just have some features disables. You can make a popup act like a regular window by enabling these features. For example, if you open a popup with
window.open('url', 'name', 'width=500, height=500, status=1, toolbar=1, location=1, menubar=1, resizable=1');
the window will have a toolbar, a URL bar, a status bar, menus, and it will be resizable. It will the same as any other window.
Keep in mind, however, that many browsers block window.open() under some conditions, and some of them will open new tabs if you specify a lot of features. Some are weird about it too; Chrome, for example, uses scroll bars on popups by default, but if you specifically tell it to use scroll bars in a popup (using scrollbars=1), it will open in a tab instead.
So basically there is no way to be completely sure that your page will always open in a new window, because browsers all handle this stuff differently, users can change settings too. The code above is probably your best bet if you have to have a new window, but you might want to look into other options.